Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors.

Yang Yang,Zachary B Smithline,Dongwei Kang,Christophe Pannecouque,Thomas A Steitz,Laura A Nguyen,Xinyong Liu,Peng Zhan

doi:10.7554/elife.36340

Abstract

Rapid generation of drug-resistant mutations in HIV-1 reverse transcriptase (RT), a prime target for anti-HIV therapy, poses a major impediment to effective anti-HIV treatment. Our previous efforts have led to the development of two novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) with piperidine-substituted thiophene[3,2-d]pyrimidine scaffolds, compounds K-5a2 and 25a, which demonstrate highly potent anti-HIV-1 activities and improved resistance profiles compared with etravirine and rilpivirine, respectively. Here, we have determined the crystal structures of HIV-1 wild-type (WT) RT and seven RT variants bearing prevalent drug-resistant mutations in complex with K-5a2 or 25a at ~2 Å resolution. These high-resolution structures illustrate the molecular details of the extensive hydrophobic interactions and the network of main chain hydrogen bonds formed between the NNRTIs and the RT inhibitor-binding pocket, and provide valuable insights into the favorable structural features that can be employed for designing NNRTIs that are broadly active against drug-resistant HIV-1 variants.

Highlights

HIV-1 reverse transcriptase (RT) plays an essential role in the viral life cycle by reverse transcribing the single-stranded RNA genome to a double-stranded DNA copy (Deeks et al, 2015; Engelman and Cherepanov, 2012)
There are two main types of RT inhibitors: nucleoside RT inhibitors (NRTIs), which act as chain terminators and compete with incoming nucleotides in the polymerase active site (Ren et al, 1998; Sarafianos et al, 1999; Tu et al, 2010; Yarchoan et al, 1988), and non-nucleoside RT inhibitors (NNRTIs), which inhibit the activity of RT noncompetitively (Merluzzi et al, 1990; Spence et al, 1995)
Emergence of drug-resistant mutations in HIV-1 RT remains a major challenge for the design and development of NNRTIs

Summary

Introduction

HIV-1 reverse transcriptase (RT) (hereinafter referred to as RT) plays an essential role in the viral life cycle by reverse transcribing the single-stranded RNA genome to a double-stranded DNA copy (Deeks et al, 2015; Engelman and Cherepanov, 2012). Etravirine (ETR, known as TMC125) and rilpivirine (RPV, known as TMC278) are two U.S Food and Drug Administration (FDA)-approved second-generation NNRTIs belonging to the diarylpyrimidine (DAPY) family (Figure 1). We demonstrated that 25a is superior to RPV in inhibiting RT bearing a wide range of resistance mutations, including K101P, Y181I and K103N/Y181I, against which RPV loses considerable potency, and determined the crystal structures of WT and mutant RTs in complex with either K-5a2 or 25a. These structures illustrate the detailed interactions between RT and the two inhibitors, and explain why K-5a2 and 25a are resilient to NNRTI-resistant mutations in the NNIBP. Our results outline the structural features of NNRTIs that can be employed for future drug design to overcome prevalent NNRTI-resistant mutations

Results

Discussion

Materials and methods